AIMC Topic: Biomedical Research

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Generalizing biomedical relation classification with neural adversarial domain adaptation.

Bioinformatics (Oxford, England)
MOTIVATION: Creating large datasets for biomedical relation classification can be prohibitively expensive. While some datasets have been curated to extract protein-protein and drug-drug interactions (PPIs and DDIs) from text, we are also interested i...

Automatic recognition of self-acknowledged limitations in clinical research literature.

Journal of the American Medical Informatics Association : JAMIA
OBJECTIVE: To automatically recognize self-acknowledged limitations in clinical research publications to support efforts in improving research transparency.

Visible Machine Learning for Biomedicine.

Cell
A major ambition of artificial intelligence lies in translating patient data to successful therapies. Machine learning models face particular challenges in biomedicine, however, including handling of extreme data heterogeneity and lack of mechanistic...

Mechanistic models versus machine learning, a fight worth fighting for the biological community?

Biology letters
Ninety per cent of the world's data have been generated in the last 5 years ( Report no. DES4702. Issued April 2017. Royal Society). A small fraction of these data is collected with the aim of validating specific hypotheses. These studies are led by ...

An attention-based BiLSTM-CRF approach to document-level chemical named entity recognition.

Bioinformatics (Oxford, England)
MOTIVATION: In biomedical research, chemical is an important class of entities, and chemical named entity recognition (NER) is an important task in the field of biomedical information extraction. However, most popular chemical NER methods are based o...

Opportunities and obstacles for deep learning in biology and medicine.

Journal of the Royal Society, Interface
Deep learning describes a class of machine learning algorithms that are capable of combining raw inputs into layers of intermediate features. These algorithms have recently shown impressive results across a variety of domains. Biology and medicine ar...

Biological Event Trigger Identification with Noise Contrastive Estimation.

IEEE/ACM transactions on computational biology and bioinformatics
Biological Event Extraction is an important task towards the goal of extracting biomedical knowledge from the scientific publications by capturing biomedical entities and their complex relations from the texts. As a crucial step in event extraction, ...